Results for the local campaign (PhD Chapter 1)
Maps and figures
This series of files compile all analyses done during Chapter 1 for the local campaign (2014):
All analyses have been done with PRIMER-e 6 and R 3.6.0.
Click on the table of contents in the left margin to assess a specific analysis.
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To assess analyses and regressions, click here.
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Caracteristics of each campaign
| 2014 | 2016 | 2017 | ||
|---|---|---|---|---|
| Sampling date | August-September | June to August | July | |
| Criteria for perturbation | Potentially impacted if close to the city or industries, References outside the bay | Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria | Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria | |
| Regions considered | BSI | BSI, CPC, BDA, MR | BSI, MR | |
| Number of sampled stations | 40 (20 HI, 20 R) | 78 (26 BSI, 19 CPC, 18 BDA, 15 MR) | 126 (111 BSI, 15 MR) | |
| Parameters sampled | Organic matter | yes | yes | yes |
| Photosynthetic pigments | no | yes | yes | |
| Sediment grain-size | yes | yes | yes | |
| Heavy-metals | yes | yes (for a limited number of stations) | no (interpolated based on 2014 and 2016 values) | |
| Benthic communities | Compartment targeted | Macro-infauna | Macro-infauna | Macro-infauna |
| Sieved used | 500 µm | 1 mm | 500 µm and 1 mm | |
| Conservation technique | Formaldehyle | Formaldehyle | Formaldehyle | |
| Others | N.A. | N.A. | N.A. |
We selected variables and characteristic species (see IndVal index and SIMPER procedure) for these analyses:
- Depth of the station: depth
- Percentage of organic matter: om
- Percentage of gravel: gravel
- Percentage of sand: sand
- Percentage of silt: silt
- Percentage of clay: clay
- Concentration of arsenic: arsenic
- Concentration of cadmium: cadmium
- Concentration of chromium: chromium
- Concentration of copper: copper
- Concentration of iron: iron
- Concentration of manganese: manganese
- Concentration of mercury: mercury
- Concentration of lead: lead
- Concentration of zinc: zinc
- Species richness: S
- Abundance of total individuals: N
- Shannon index: H
- Piélou evenness: J
- Abundance of Bipalponephtys neotena: Bneo
- Abundance of Spisula solidissima: Ssol
Here, we use data from subtidal ecosystems (see metadata files for more information).
Only stations that have been sampled both for abiotic parameters and benthic species were included.
1. Maps
1.1. General map
1.2. Parameters maps
For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity.
OM
Gravel
Sand
Silt
Clay
Arsenic
Cadmium
Chromium
Copper
Iron
Manganese
Mercury
Lead
Zinc
Bneo
Pste
Ssol
Epar
Species richness
Total abundance
Shannon index
Piélou’s evenness
2. Figures
2.1. Barplots
Organic matter
Grain-size
Heavy metals
Species abundances
Diversity indices
2.2. Phylum frequencies
| Phylum | HI | R |
|---|---|---|
| Annelida | 20340 | 1042 |
| Phoronida | 1138 | 2 |
| Arthropoda | 871 | 746 |
| Mollusca | 341 | 725 |
| Platyhelminthes | 5 | 0 |
| Echinodermata | 4 | 139 |
| Hemichordata | 2 | 0 |
| Brachiopoda | 0 | 0 |
| Cnidaria | 0 | 0 |
| Nematoda | 0 | 0 |
| Nemertea | 0 | 5 |
2.3. Species estimation curves
2.4. Principal Component Analysis
Parameters + Metals
Variables have been scaled by mean and standard-deviation prior to analysis.
Parameters
Variables have been scaled by mean and standard-deviation prior to analysis.
Metals
Variables have been scaled by mean and standard-deviation prior to analysis.
2.5. Non-metric Multidimensional Scaling
Parameters + Metals
Variables have been scaled by mean and standard-deviation prior to analysis.
Parameters
Variables have been scaled by mean and standard-deviation prior to analysis.
Metals
Variables have been scaled by mean and standard-deviation prior to analysis.
Species
Stations with no species are deleted from this analysis.
2.6. Hierarchical Agglomerative Clustering
Parameters + Metals
Variables have been scaled by mean and standard-deviation prior to analysis.
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
## 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 3 2 2 2 1 2 2 2 2 2 3 2 2 2 3 3 2 3 2 3 2
## 37 38 39 40
## 2 2 2 2
Parameters
Variables have been scaled by mean and standard-deviation prior to analysis.
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
## 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 3 3 3 3 3 2 3 3 2 2 2 3 2 3 2 3
## 37 38 39 40
## 3 3 3 3
Metals
Variables have been scaled by mean and standard-deviation prior to analysis.
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
## 1 2 1 1 1 1 2 1 1 1 2 3 2 2 2 3 3 2 2 2 2 2 2 3 2 3 3 3 3 3 3 3 3 3 3 2
## 37 38 39 40
## 2 3 3 3
Species
Stations with no species are deleted from this analysis.
## 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
## 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
## 37 38 39 40
## 2 2 2 2
